Different camera settings for different render layers?
You can have multiple cameras, but only one can be used at a time.

As a workaround, you can use two scenes.


Move the object to be rendered in Perspective to the first layer and the object to be rendered in Orthographic to the second layer.

Go to the Layers tab and select Layer 1 to be rendered.


Create a new scene by clicking the + in the Info Panel:



Select Link Objects.
In the new scene, select the camera and press U> Object and Data to make the camera's transforms and settings independent from the original scene.  Then set the camera to be orthographic in Properties > Object data > Lens.
Still in the new scene, go to the Layers tab and select Layer 2 to be rendered. 
Set the background to transparent by enabling Transparent in Render settings > Film.
In the composite nodes (for either scene, just keep in mind that they are independent so it's easiest to keep all the nodes in one scene) duplicate the Render Layers node and pick the other scene:


You can now combine them however you want using the compositor. E.g. with an Alpha Over node:




In this render, Suzanne is in orthographic and the rest is in perspective.